CARROT ENDOPHYTES: DIVERSITY, ECOLOGY AND FUNCTION

Endophytes are a unique
group of microorganisms that spend at least part of their life cycle within
plant tissues. These microbes are increasingly being recognized for their
potential to improve the health and productivity of their host plants. Recent
studies indicate that endophytes could also influence human health by altering
the composition of chemical compounds within plants, thereby affecting their
nutritional quality and flavor. In addition, the presence of endophytes in
edible plant tissues could directly affect human health by introducing microbes
that can stimulate the immune system or act as opportunistic pathogens in
people with compromised immune systems. However, despite their potential
importance for plant and human health, these plant-associated microbes have
been understudied due to a lack of visible symptoms associated with their
presence and difficulty in isolating them from plant tissues. In the present
studies, we hypothesized that endophytes play an important role in carrot, one
of the most important vegetable crops in the world.

Carrot is well known as an important source of
vitamins, antioxidants and other nutrients in the human diet, and carrot
taproots are often consumed raw. Carrot crops are slow to establish and are subject
to assault by a wide range of pests that negatively affect the health and
productivity of this crop, as well as the storage potential of its taproots.
Consequently, the aim of these studies was to examine endophyte dynamics in
carrot. Studies were carried out in field, greenhouse and laboratory trials
using a diverse set of carrot genotypes with broad genetic backgrounds and
physiological characteristics. Endophyte communities were studied using
traditional culture-based techniques, along with low and high throughput
sequencing technologies.

Results of these studies
demonstrate that carrot seeds and taproots are colonized by an abundant and
diverse set of endophytic microbial taxa. Many of these endophytes could
solubilize phosphorous, fix atmospheric nitrogen, produce siderophores and
auxin and suppress infection by a key carrot pathogen, Alternaria dauci, demonstrating their potential importance for
maintaining carrot health and productivity. Some of the endophytes identified
in these trials were vertically transmitted to progeny inside carrot seeds,
indicating that they could be part of a core microbiome that evolved alongside
carrot plants, and are likely to be critical in early seedling establishment.
We also determined that carrot endophytes could be acquired via horizontal
transmission from soil with greater soil health in an organic relative to a
conventionally managed system resulting in greater populations of endophytes
with antagonistic activity against A.
dauci. Finally, endophyte communities varied among the genotypes evaluated
in this study, with some being more responsive to the presence of greater
populations of beneficial endophytes in their environments. This indicates that
it could someday be possible to begin selecting for these beneficial plant
microbial relationships in breeding programs.

Based on the results of these studies, we
conclude that endophytes do indeed play an important role in carrot. Additional
research aimed at determining how these microbes functionally interact with
carrot plants and identifying practical approaches to manipulate these
communities to enhance the productivity and quality of carrot taproots, are
recommended. A new isolation technique identified in these trials will aid in
these efforts.